Extract rows present in file1 and not in file 2
Hello everyone,
I have 2 tab separated files and I want to compare them on the basis of chr,start,ref and alt and print only the rows of file1 that aren't present in file2 in the output file. please see below.
file1:
chr start ref alt freq
1 11906040 C T 2.76E-05
1 11906049 C T 2.76E-05
1 11906068 A G 0.147142
1 11907124 C T 2.77E-05
1 11907125 C G 0.000471777
1 11907703 AAGG A 2.78E-05
1 11907717 CGGT C 5.59E-05
File2:
chr start end ref alt freq
1 12198 12198 G C .
1 12237 12237 G A .
1 12259 12259 G C .
1 12266 12266 G A .
1 12746 12773 GGGAGTGGCGTCGCCCCTAGGGCTCTAC - 0
1 12745 12773 TGGGAGTGGCGTCGCCCCTAGGGCTCTAC T 0
1 11907703 AAGG A 2.78E-05
1 11907717 CGGT C 5.59E-05
output file:
chr start ref alt freq
1 11906040 C T 2.76E-05
1 11906049 C T 2.76E-05
1 11906068 A G 0.147142
1 11907124 C T 2.77E-05
1 11907125 C G 0.000471777
thanks in advance.
Regards,
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ijlal.hyder2012 •
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2 answers
From your example inputs and output, it can also be:
$ grep -v -f file2.tab file1.tab
chr start ref alt freq
1 11906040 C T 2.76E-05
1 11906049 C T 2.76E-05
1 11906068 A G 0.147142
1 11907124 C T 2.77E-05
1 11907125 C G 0.000471777
But only if the format in your file2 is correct,
since the last two rows in your file2 are with 5 fields, not 6 (no end).
$ awk '{print NF}' file2.tab
6
6
6
6
6
6
6
5
5
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